Overview

• Total strains : 1,238
• Total SNVs before filter : 5,065,794
• Total SNVs after filter : 2,970,933
• Total indels before filter : 1,908,754
• Total indels after filter : 611,052

Site-level quality filters

Number of variant sites removed by each filter

Each bar shows counts of variant sites removed by the combinations of filters indicated by the dots below.

Pre-filter statistics

Variant counts for each strain based on vcf containing all variant sites called by GATK (“soft-filter.vcf”).

Post-filter statistics

Variant count for each strain based on the VCF containing only sites pass all filters (“hard-filter.vcf”). All heterozygous sites on main chromosomes were converted to either homozygous or missing. The remaining heterozygous sites are all located on mitochondria chromosomes.

Relationship between heterozyous SNVs and total SNVs

Number of variants versus the number of heterozygous calls shows strains that might have mixed genotypes or low quality calls (high het but low variation).